This blog chronicles the research of the UsefulChem project in the Bradley lab at Drexel University. The main project currently involves the synthesis of novel anti-malarial compounds. The work is done under Open Notebook Science conditions with the actual detailed lab notebook located at usefulchem.wikispaces.com. More general comments posted here relate to Open Science, especially when associated with chemistry.

Monday, August 20, 2007

First SciFoo Lives On Session

We had our first SciFoo Lives On session today on Nature Island (Second Nature) in Second Life. We had about a dozen people participate.

The topic was "Tools for Open Science". I wanted to explore more fully the actual technology that people are starting to use towards doing more open science. I started off by showing screenshots of UsefulChem wiki and blogs from my poster. The other posters there (and still there) included MyExperiment, Nature Precedings, Bill Hooker's Thoughts, Knowble and Connotea.

Overall it went very well I think. Initially I was disappointed that most people did not have voice working but it turned out to be a good thing because I was able to capture the entire chat transcript (see below).

Based on Berci's suggestion, we'll do "Medicine and Web 2.0" next week on Monday Aug 27, 2007 ET noon. So bring your posters and join us!

Here is the transcript: [9:00] You: I think many of you were at scifoo[9:00] You: one of the problems is ther was not enough time to cover everything[9:01] You: this is a continuation on that[9:01] You: on Tools for Open Science[9:01] You: this really should be a discussion[9:01] You: so we'll just take a few minutes each to explain[9:01] You: I'll start on the Open Notebook Science poster[9:02] You: then we'll go to the right and around the corner[9:02] You: please stop me if you have a comment or question[9:02] You: I was hoping to do this by voice but not enough people have it[9:03] Max Chatnoir: good to have the chat record.[9:03] Berci Dryke: sure[9:03] You: what I would like for my 5 mins is to show screenshots of our Open Notebook Science[9:03] You: so we have one component that is a blog[9:04] You: the idea is to record everything from ongoing research in my lab[9:04] You: I'm skipping over stuff because I don't want to take 1 hour :)[9:04] You: we started tracking molecules in my lab using a blog like this[9:05] You: but now we are moving this to Chemspider[9:05] Stew Alito: Um.... can Phoenix move to the side a bit? It's the wings... can't see![9:05] Berci Dryke: lol[9:05] You: we started tracking experimnents using a blog[9:05] You: but there were too many edits[9:05] Troy McLuhan: To adjust your camera position, hold down ALT and then click-drag with your mouse[9:05] You: so we moved to a wiki[9:06] You: the wiki has all the lab notebook pages and organization pages[9:06] You: the wiki tracks nicely the contribution of everybody over time[9:06] You: and we can prove who-knew-what-when[9:06] You: with each version[9:07] You: we use Wikispaces because it is free and offers thridparty time stamps[9:07] Max Chatnoir: These are suggestions for the synthesis?[9:07] You: which one max?[9:07] You: there were comments from others yes[9:08] You: but it turns out our collaborators prefer to use our mailing list to share[9:08] You: so the wiki is mainly my students in the lab[9:08] You: I will leave the rest here - tha's it for me[9:08] You: any comments/questions?[9:08] Berci Dryke: What about competition?[9:09] You: you mean fear of being scooped berci?[9:09] Berci Dryke: yes[9:09] You: I think that this is safer than many other things scientists do[9:09] You: like proposals[9:09] You: because all this is indexed quickly in google[9:10] You: it would be very embarrasing to get caught stealing text[9:10] Max Chatnoir: So this is a sort of ongoing multicontributor proposal presentation?[9:10] Max Chatnoir: But very publicly documented![9:10] Stew Alito: Have you ever been scooped, to your knowledge?[9:10] You: max this simply our standard lab notebook on a public wiki[9:10] You: no I don't know of anyone having "stolen" anything[9:11] Max Chatnoir: So the contributors are mostly your own students?[9:11] You: max - yes the wiki is mainly my students[9:11] Berci Dryke: your wiki can be edited by anyone (or just those who have access to it?)[9:11] You: on the mailing list we have great collaborators like[9:11] Max Chatnoir: Do you get external contributions as well?[9:11] You: Rajarshi Guha that does docking for us[9:11] You: max - you have to register[9:12] Troy McLuhan: Which mailing list service/software do you use?[9:12] You: simply because otherwise my students forget to login![9:12] Max Chatnoir: But the registration is open?[9:12] You: we use Google groups[9:12] suhky Rezillo: now I am here[9:12] You: we are ALL google - blog, wiki, lists[9:12] Berci Dryke: why is better than creating an own wiki (I mean used in an internal network)[9:12] Max Chatnoir: Like WebCT?[9:12] You: Google has been a huge gift to open science[9:12] You: what is like webct maX?[9:13] Max Chatnoir: Internal network.[9:13] Stew Alito: Do you share references with Zotero or Connotea etc.?[9:13] Max Chatnoir: I was adding to Berci's question.[9:13] You: I have used Connotea with my class students[9:13] You: but not systematically[9:13] Rakerman Yellowjacket: I wonder about the amount of information - do you think there's any difference between someone getting a protocol from your notebook, or a "refined" version from myExperiment or Nature Protocols?[9:14] You: good point raker[9:14] Corwin Carillon is Offline[9:14] You: Nature protocols is great for established protocols[9:14] You: but it takes time to get the info in there[9:14] You: UsefulChem is real time so by necessity messy[9:14] You: BUT - the question is can scientist use the info[9:15] You: and based on the types of searches we observe - I say yes[9:15] You: we can always collect and publish these as full papers later[9:15] Rakerman Yellowjacket: I am wondering - if everyone published their lab notebooks online, what would google search results look like - how would be be able to find the most relevant results? Would online notebooks s scale?[9:15] You: well we have to add metadata[9:15] Adastar Galsworthy: how do people feel about citing online resources?[9:15] Max Chatnoir: So this is one way to get "tried this, didn't work" into a publicly accessib le space.[9:16] You: for example in chemistry we tag with inchis[9:16] Adastar Galsworthy: particularly informal resources[9:16] You: each field will have to add metadata[9:16] You: do we have our myexperiment guy here?[9:17] You: ok, someone want to say a few words about Precedings?[9:17] You: we can move to that poster[9:17] Max Chatnoir: Can people not in your class register for the wiki?[9:17] You: max - yes they can[9:18] You: suhky?[9:18] suhky Rezillo: yes?[9:18] Max Chatnoir: So, Berci, that would be why it is in a public forum rather than an internet network like WebCT or Blackboard.[9:18] You: would you like to say a few words about precedings[9:18] Berci Dryke: understood, Max :)[9:19] Joanna Wombat: Hilary's just coming now[9:19] You: I've use precedings myself[9:19] Joanna Wombat: I think she can say something about precedings[9:19] suhky Rezillo: one moment Hilary will talk about Nature Precedings as she co-developed the site...[9:19] You: and I think it is a fantastic addition to tools for open science[9:19] You: oh good[9:19] Max Chatnoir: Indeed![9:19] Hilary Serevi: hi everyone[9:19] Troy McLuhan: Would it make sense to publish the transcript of this discussion on Nature Preceedings?[9:19] Joanna Wombat: Hi Hilary[9:19] You: hilary you have the floor[9:19] suhky Rezillo: Everyone, let me well you to Hilary Serevi[9:20] Berci Dryke: nice to meet you![9:20] Hilary Serevi: thanks--I haven't spent too much time in second life[9:20] Hilary Serevi: but hopefully I can answer some questions about Precedings[9:21] You: hilary what was your role in precedings[9:21] You have offered friendship to Krystine Qinan[9:21] Hilary Serevi: I'm the Product Development Manager[9:21] Krystine Qinan is Online[9:21] You: did you make this poster?[9:22] suhky Rezillo: Yes she did, with Timo Hannay[9:22] Hilary Serevi: yes[9:22] You: anyone else here use precedigns?[9:22] Troy McLuhan: Can you summarize what it is?[9:22] You: basically you can publish in any format[9:22] You: the submissions are editorially reviewed[9:22] You: but not peer reviewed[9:23] Hilary Serevi: that's correct, Horace[9:23] You: but it does not have to be an article format[9:23] You: I have published blog posts there[9:23] You: well the poster will stay there after this session[9:23] Berci Dryke: can I have a personal question about it?[9:23] yucca Gemini is Online[9:23] You: yes berci[9:23] Berci Dryke: I'm a medical student and have a presentation about web 2.0 and medicine (Medicine 2.0). Why would it be good for me to publish it on Precedings? And could I publish it?[9:24] You: they do have a lot of presentations[9:24] You: I published my ppt as well that we were loking at[9:24] You: let's move on[9:24] You: Bill could not make it[9:24] You: so I'll say a few things[9:25] Stew Alito is Offline[9:25] You: Bill Hooker has been reporting on Open Science for a long time[9:25] Hilary Serevi: since we've moved on, perhaps I can answer your question later, berci[9:25] You: and he asked me to ask you about what you thought about the def o open science[9:25] Berci Dryke: ok, Hilary[9:25] You: sorry hilary[9:26] You: please answer[9:26] You: does anyone have thoughts about the definitions?[9:27] You: the term open science has been used so much we don't know what it means somtimes[9:27] Samara Barzane is Online[9:27] Rakerman Yellowjacket: it's more like "publically shared pre-publication science"[9:28] Adastar Galsworthy: i have a thought about the reasons for the need for open science[9:28] Troy McLuhan: PLoS is open though, and is for publication[9:28] Adastar Galsworthy: I think it was in the middle of the 18th century that the last man to have read everythin lived,[9:28] Emile Pintens: Rakerman, I do not know if that it has to be pre-published. I think the ultimate goal would be for pre-published, and published works to be open.[9:29] You: so you don't consider precedings to be "published"[9:29] You: according to patent law that is certainly a publication[9:29] Hilary Serevi: so precedings doesn't "publish" documents--they'i think that the term "open access" tends to be applied to peer-reviewed publication[9:29] You: it is not peer-reviewed[9:29] Troy McLuhan: Sorry, that's what I mean[9:30] Hilary Serevi: i think the definition of a "publication" is changing with the development of the internet[9:30] You: so when people say pre-publication they mean pre-peer-reviewed[9:30] Emile Pintens: Isn't Precedings screened? It isn't peer-reviewed, but it is reviewed[9:30] Rakerman Yellowjacket: pre-peer-reviewed is maybe a better term[9:30] Troy McLuhan: I guess what I really mean is, does the tenure review committee consider it "published"?[9:30] You: definition confusion was big at scifoo i think[9:30] Hilary Serevi: It's screened, but the screening process is mainly to prevent the posting of obviously commercial documents (e.g. spam)[9:31] Hilary Serevi: or pseudoscience[9:31] Hilary Serevi: although pseudoscience is also another term that is difficult to devine[9:31] Hilary Serevi: define--sorry[9:31] You: but without defining "peers", it is hard to define peer review[9:31] Emile Pintens: Ok thank you for the clarification. Is there a time lag between an item being submitted and the time it makes it on the site?[9:31] Adastar Galsworthy: in peer reviewed journals there is plenty of pseudo-science. that was my experience as an editor for a few smaller physics journals for a while[9:32] Hilary Serevi: yes--the mean time between submission and posting is less than a day[9:32] DrDoug Pennell is Offline[9:32] You: yes precedings made me change my abstract to they did read it![9:32] Adastar Galsworthy: I'd like to jump the discussion back a few rungs[9:32] Max Chatnoir: That's a really fast turnaround.[9:33] suhky Rezillo: Horace - what or how much do you submit to precedings?[9:33] Adastar Galsworthy: less about the specifics of what the mechanics of open science are, and discuss the issue of accreditation[9:33] You: suhky - I only submitted 3 times[9:33] Troy McLuhan: Preceedings is quite new I think[9:33] Hilary Serevi: it's because we don't send the submissions out to scientists currently working in the field[9:33] Emile Pintens: Change the abstract? Thats the first time I've heard of that happening in Preceedings[9:33] You: Emile - well they had some good points[9:34] Emile Pintens: Ah gotcha[9:34] Troy McLuhan: Adastar - What do you mean by accreditation?[9:34] You: told me to be more explicit[9:34] Max Chatnoir: The fact that there is some editorial review should carry some weight with things like tenure committees.[9:34] You: absolutely max[9:34] Adastar Galsworthy: the point someone raised earlier about the leve of acceptance by tenure committees and so forth.[9:34] You: we have to explain it to the tenure committees[9:35] Hilary Serevi: Adastar--is your question about whether accredation is a prerequisite for participation in open science?[9:35] Emile Pintens: The question is how long with the tenure committees take in accepting Web 2.0 tools like the ones we are talking about[9:35] Emile Pintens: How long will*[9:36] You: it is certainly an issue (accreditation) and that is why it is important that we continue to talk[9:36] You: we will need each other to support what we are doing[9:36] Max Chatnoir: I would think that this kind of publication would at least have the status that a presentation at a meeting would have.[9:36] You: to explain, to validate[9:37] You: max that is true presentations count and are not peer reviewed[9:37] Adastar Galsworthy: I'm working for Nature, and there is certainly belief within this comapny that such metrics will emerge.[9:37] Max Chatnoir: Also, you're putting your work out in a very public venue, so there is a very wide potential peer pool for comments.[9:37] Troy McLuhan: I don't think it's a matter of accepting tools. Scientists are always bringing new tools into use. It's a matter of determining "what counts". For example, the recent proof of the Poincare Conjecture was never published in a Peer Reviewed journal as far as I know, but certainly "counts"[9:37] You: adastar - we are looking for Nature to take some lead in that[9:38] Emile Pintens: Adastar, metrics from where?[9:38] Hilary Serevi: there's an interesting paper by the PLoS medicine editors about how impact factor will change in response to web 2.0 tools[9:38] Berci Dryke: Hilary: could you please give a link to that?[9:38] Hilary Serevi: troy's reference is to Perelman's use of ArXiv rather than a math journal to distribute his work[9:38] You: hilary - yes Heather Piwooar[9:38] You: piwowar[9:38] Hilary Serevi: doi: 10.1371/journal.pmed.0030291[9:39] Berci Dryke: thank you[9:39] Hilary Serevi: the chronicle of higher education also had an article about that[9:39] Hilary Serevi: i don't have the link available[9:39] Rakerman Yellowjacket: I think scientists need to push back against impact factor and move to a concept of "science portfolio" - what work have you done - there are going to be all different types of contributions[9:39] Adastar Galsworthy: at the moment we are building social tools, but they are mostly in their first generation[9:40] You: racker very good point - metrics are limited compared to portfolios[9:40] Adastar Galsworthy: the obvious things to start looking for are the spoead of influence of ideas through social networks[9:40] Adastar Galsworthy: but there is a bit of a way to go before anything solid is around to this robustly[9:40] You: but we can still play with metrics - let just not give everything else up[9:41] Adastar Galsworthy: however, I want to stress that I feel the reason that we need to do this is so that we can support open science, which I happen to think is vital in the presence of too much information to sift through[9:41] Adastar Galsworthy: open science goes hand in hand with social networking, and this provides a platform for collaborative filtering[9:42] You: Ada - do you wnat to talk about Connotea/Emile about Knowble[9:42] suhky Rezillo: Doesn't Connotea acknowledge users' contribution to the site?[9:42] Rakerman Yellowjacket: ISI algorithms shouldn't be the end-all of evaluating a scientist for tenure and promotion - we already have a system to evaluate grants - tenure committees should recognize the full work of the scientist - SOME of which must pass both the review of peers and hopefully be tested through being reproduced[9:42] Emile Pintens: I can talk about Knowble anytime[9:42] Emile Pintens: Am I next?[9:42] You: sure[9:43] Emile Pintens: Knowble is a knowledge community for researchers to connect, communicate, and collaborate.[9:43] You: hold on[9:43] Emile Pintens: ok[9:44] You: sorry emile not for you - go on[9:44] You: brb[9:44] Emile Pintens: O ok, sorry.[9:45] Emile Pintens: I came up with the idea while I was an undergrad at UNC, and we received funding from the School of Medicine as a part of UNC's CTSA proposal.[9:45] Emile Pintens: Right now we are in Beta, but the idea is to provide a common community where researchers, professors, and scientists may connect based upon common research areas or methodologies.[9:45] Max Chatnoir: Brilliant, Emile.[9:45] You: I've tried Knoble recently[9:45] Troy McLuhan: Wow this is a great idea[9:45] Berci Dryke: is it similar to Tiromed.com?[9:46] You: to specify our need for a docking expert[9:46] Hilary Serevi: Over here![9:46] Emile Pintens: We are taking an approach similar to Facebook where we must accept your institution before a person may be able to register.[9:46] Emile Pintens: I have not seen Tiromed.com[9:46] Emile Pintens: Hilary, you have a question?[9:46] Max Chatnoir: I just discovered that, Emile![9:46] Berci Dryke: that is a medical community site with the same goals[9:46] Hilary Serevi: sorry - no[9:47] suhky Rezillo is Offline[9:48] You have offered friendship to Troy McLuhan[9:48] Troy McLuhan is Online[9:48] Emile Pintens: Ah ok. While the School of Medicine provided the initial funding, we are moving to allow researchers from really any discipline to join. Our tools are not at the level of any discipline, but we are working on it. An example, we are linked to PubMed, which some professors at UNC feel it does not include all of their works.[9:48] Rakerman Yellowjacket: how does knowble compare to pronetos and other scholar community sites?[9:48] You have offered friendship to Rakerman Yellowjacket[9:48] Rakerman Yellowjacket is Online[9:48] You have offered friendship to Xantha Oe[9:49] You have offered friendship to Joanna Wombat[9:49] You have offered friendship to Hilary Serevi[9:49] Emile Pintens: From what we know about Pronetos, they are focused on Publishing. We are focused on connecting people.[9:49] Hilary Serevi is Online[9:49] Emile Pintens: But since Pronetos isn't online yet, I do not know for sure, but we wish them luck![9:50] Troy McLuhan: I gather that Knowble is mainly for scientists and academics, as opposed to the general public with an interest in science?[9:51] Joanna Wombat is Online[9:51] Xantha Oe is Online[9:51] Emile Pintens: Right now yes. We are trying to ensure a fairly tight user base. In time, I would not count us out in opening up to the general public.[9:52] Emile Pintens: We are in beta, so user feedback is being gathered and we will be making further changes in the coming weeks.[9:52] Emile Pintens: Are there any further questions?[9:52] You: Ada do you want to say something about Connotea[9:52] Adastar Galsworthy: sure[9:52] Troy McLuhan: What is the underlying development tools for Knowble? A CMS? A web language?[9:53] Emile Pintens: Troy, we use LAMP[9:53] Adastar Galsworthy: first, sorry about the mess[9:53] Visitor Counter 1.8: Welcome Xantha Oe. You have been counted.[9:53] Adastar Galsworthy: I just threw these together 1/2 an hour ago.[9:53] Visitor Counter 1.8: Welcome Berci Dryke. You have been counted.[9:53] Adastar Galsworthy: am giving a talk on friday and will post the full presentation here in a nice format next week,.[9:54] You: thanks ada[9:54] Adastar Galsworthy: as many of you know there are a bunch of tools for bookmarking on hte internet[9:54] Adastar Galsworthy: the great grand daddy is delicious.[9:54] Adastar Galsworthy: Nature, and me spcifically, work on a tool for scientists called connotea[9:55] Adastar Galsworthy: there are about three other specific tools out there for scientists.[9:55] Adastar Galsworthy: I'd say take em for a test drive and pick the one you like best (as long as it's conotea ;)[9:56] Adastar Galsworthy: as I was alluding to earlier, one of the things we are trying to do with connotea is make it into a rccomendation engine for scientsits[9:56] Adastar Galsworthy: to help filter the huge number ot papers out there[9:56] Adastar Galsworthy: but it is early days yet[9:56] Adastar Galsworthy: There is an api and some people have bulit some cool apps using conontea as an engine[9:56] You: what is an example ada[9:57] Adastar Galsworthy: most of the exentions are greasmonkey extensions.[9:57] Hilary Serevi: can you use greasemonkey to connect to the api?[9:57] Adastar Galsworthy: one called Stack it, creates digg like buttons next to doi's on any poge and lets you see if the paper has been bookmarked[9:58] Adastar Galsworthy: another called the entity describor (which was just provisionally released last week, so give it another week or so)[9:58] Adastar Galsworthy: connects tags in conntea to a structured ontology, such as the MeSH ontology[9:59] Adastar Galsworthy: There is another that uses conntoea as a backbone for connecting XML stlysheets for scehmas representing systems biology7[9:59] Adastar Galsworthy: you can see them at http://www.connotea.org/wiki/ConnoteaTools [9:59] You: Ada - do you think you would be able to take Nature Predecings posts in connotea[9:59] Adastar Galsworthy: yes, we are working on that[10:00] Adastar Galsworthy: rather than waiting for everything to be perfect our philosophy is torelease and improve[10:00] You: that would really help push the more open side[10:00] You: thanks adastar![10:00] Adastar Galsworthy: no probs.[10:00] You: before we go -[10:00] You: any suggestions for the theme of the next session?[10:00] Berci Dryke: medicine and web 2.0 :)[10:01] You: nice berci[10:01] Max Chatnoir: Horace, it it always in this time block?[10:01] Hilary Serevi: i'm very intested in the ethical issues associated with putting medical(theraputic/clinical) infomation on the web[10:01] You: max I think same time next week[10:01] Adastar Galsworthy: I gotta go now, thank's guy's[10:01] Berci Dryke: Hilary: this is a crucial question...[10:01] Adastar Galsworthy is Offline[10:01] Hilary Serevi: thanks for organizing horace[10:01] You: I'll post the transcript also on usefulchem.blogpspot.com[10:01] You: sure my pleasure[10:02] Berci Dryke: thank you, Horace![10:02] Max Chatnoir: Sigh.... I'll have a class then, but will look for the TS![10:02] You: thank you all![10:02] Berci Dryke: I'll also post about it with many images[10:02] Max Chatnoir: Excellent, Berci.[10:02] You: yes please send me you images it you want[10:02] You: we'll leave these posters up[10:02] Max Chatnoir: Got a RL faculty meeting. Thanks, Horace![10:02] Emile Pintens: I have already made a post in the Knowble blog! http://www.knowble.net/blog/[10:03] Berci Dryke: next week, same time?[10:03] You: so Berci lets do that then[10:03] You: yes same time[10:03] Emile Pintens: Same time next week sounds good[10:03] You: thanks to joanna too for the space![10:03] Hilary Serevi: nice meeting everyone[10:03] Hilary Serevi: thanks again![10:03] Joanna Wombat: thanks![10:03] You: bye everyone[10:04] Berci Dryke: Bye![10:04] Emile Pintens: thanks Jean-Claude this was great! Talk to you soon[10:04] Max Chatnoir is Offline[10:04] Joanna Wombat is Offline[10:05] Troy McLuhan: If you're interested in science-related events in SL, feel free to join the Science Center group[10:05] Emile Pintens: Troy how do we do that?[10:05] Rakerman Yellowjacket: thanks Jean-Claude